[gmx-users] Re: Notes and warnings using grompp

[Justin Lemkul]

On 9/28/12 5:13 PM, Sonia Aguilera wrote:
> Hi,
>
> I understand that usually it is needed to add counterions . I´m performing a
> free energy calculation and I want to see the free energy change without
> adding the ions. What I´m asking is why the program reads a total charge of
> -13.000002 not 13.0. The note says that it must be an integer, but I don´t
> know what to change or where. Should I ignore the note?
>

grompp reads a net charge of -13 because that's the charge (almost certainly) on 
the protein, per the parameters in the topology.  -13.000002 is close enough to 
an integer that the minor difference is due to rounding, as the link I provided 
before states.  Whether or not you ignore it depends on whether or not you think 
whatever you are modeling is reasonable.

> I have seen (second note) that since it is just a note, it can be ignored,
> but according with the parameters of the note, what do you think?
>

Notes are there to warn you that something is potentially wrong.  It looks like 
either your .mdp settings are inappropriate or you have a large charge group. 
This situation can lead to artifacts from incorrect neighbor searching or 
nonbonded calculations.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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